GgaINT1010132 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9067992-9068335:+
Coord C1 exon
chr12:9067992-9068117
Coord A exon
chr12:9068118-9068188
Coord C2 exon
chr12:9068189-9068335
Length
71 bp
Sequences
Splice sites
5' ss Seq
ACGGTACCG
5' ss Score
7.03
3' ss Seq
TGATGTGCGGCCCTTGGCAGGGG
3' ss Score
5.1
Exon sequences
Seq C1 exon
CAGCTGAGCAGGTGGGGACAGTATCCCGGTTGGAGGTGCAGTCATCCAGGAGCAATGTTGCCCGTGTCACCTGGGTCGGTGTGCCGGGAGCCACAGCGTACCGTGTGGTGTGGAGCCGTCGGGACG
Seq A exon
GTACCGTGGGATGAGGACGGGTGGGGACGGCAATGATGGTGGCACCAGGGCTGATGTGCGGCCCTTGGCAG
Seq C2 exon
GGGGCTCGGAGAGGAGCCAGCATGTTCCTGGCCACATCAGCTCCTTCGACATCCCCGACCTGGAGGGAGGTGTCTCCTACACTGTGAAGGTCACAGCACTCATAGGCAACCATGAAGGCAACCCCGTGTCCATCATCGTCACCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.256 A=NA C2=0.400
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=86.0)
A:
NA
C2:
PF0004116=fn3=PD(51.9=82.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGCAGGTGGGGACAGTATC
R:
GGGATGTCGAAGGAGCTGATG
Band lengths:
177-248
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]